9-136745852-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198946.3(LCN6):c.293A>T(p.Glu98Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000831 in 1,613,466 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198946.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LCN6 | NM_198946.3 | c.293A>T | p.Glu98Val | missense_variant | Exon 3 of 7 | ENST00000341206.9 | NP_945184.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LCN6 | ENST00000341206.9 | c.293A>T | p.Glu98Val | missense_variant | Exon 3 of 7 | 1 | NM_198946.3 | ENSP00000339621.3 | ||
ENSG00000204003 | ENST00000435202.5 | n.263A>T | non_coding_transcript_exon_variant | Exon 3 of 11 | 2 | ENSP00000399627.1 |
Frequencies
GnomAD3 genomes AF: 0.000434 AC: 66AN: 152140Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000995 AC: 25AN: 251362Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135876
GnomAD4 exome AF: 0.0000465 AC: 68AN: 1461208Hom.: 0 Cov.: 30 AF XY: 0.0000344 AC XY: 25AN XY: 726928
GnomAD4 genome AF: 0.000433 AC: 66AN: 152258Hom.: 0 Cov.: 30 AF XY: 0.000403 AC XY: 30AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.293A>T (p.E98V) alteration is located in exon 3 (coding exon 3) of the LCN6 gene. This alteration results from a A to T substitution at nucleotide position 293, causing the glutamic acid (E) at amino acid position 98 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at